FAIRMol

NMT-TY0920

Pose ID 13891 Compound 544 Pose 333

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T21
T. cruzi R5P T. cruzi
Ligand NMT-TY0920
PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
31.6 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.67
Burial
81%
Hydrophobic fit
66%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.219 kcal/mol/HA) ✓ Good fit quality (FQ -11.50) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Very high strain energy (31.6 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (13) ✗ Many internal clashes (12)
Score
-34.121
kcal/mol
LE
-1.219
kcal/mol/HA
Fit Quality
-11.50
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
31.6 kcal/mol
SASA buried
81%
Lipo contact
66% BSA apolar/total
SASA unbound
597 Ų
Apolar buried
320 Ų

Interaction summary

HB 11 HY 10 PI 2 CLASH 6

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.430Score-34.121
Inter norm-0.961Intra norm-0.257
Top1000noExcludedno
Contacts17H-bonds11
Artifact reasongeometry warning; 12 clashes; 13 protein contact clashes; high strain Δ 31.6
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 ARG113 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap14Native recall1.00
Jaccard0.82RMSD-
HB strict6Strict recall0.50
HB same residue+role6HB role recall0.67
HB same residue5HB residue recall0.62

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
302 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 0 0.00 0.00 - no Open
320 1.0669444827431311 -0.878088 -31.4505 3 16 0 0.00 0.00 - no Open
345 1.1134646347622539 -0.877657 -23.1229 3 15 0 0.00 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 0 0.00 0.00 - no Open
333 2.430240854014312 -0.961348 -34.1213 11 17 14 1.00 0.67 - no Current
313 2.7355217655896267 -0.945999 -28.0195 7 18 0 0.00 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 0 0.00 0.00 - no Open
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 0 0.00 0.00 - no Open
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 16 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -34.121kcal/mol
Ligand efficiency (LE) -1.2186kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.504
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -34.78kcal/mol
Minimised FF energy -66.37kcal/mol

SASA & burial

✓ computed
SASA (unbound) 596.9Ų
Total solvent-accessible surface area of free ligand
BSA total 485.8Ų
Buried surface area upon binding
BSA apolar 320.2Ų
Hydrophobic contacts buried
BSA polar 165.7Ų
Polar contacts buried
Fraction buried 81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2155.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 758.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)